+Open data
-Basic information
Entry | Database: PDB / ID: 1l8a | |||||||||
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Title | E. COLI PYRUVATE DEHYDROGENASE | |||||||||
Components | Pyruvate dehydrogenase E1 component | |||||||||
Keywords | OXIDOREDUCTASE / THIAMIN DIPHOSPHATE / PYRUVATE / ALPHA-KETO ACID DEHYDROGENASE | |||||||||
Function / homology | Function and homology information : / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity ...: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / glycolytic process / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / membrane / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | |||||||||
Authors | Furey, W. / Arjunan, P. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution. Authors: Arjunan, P. / Nemeria, N. / Brunskill, A. / Chandrasekhar, K. / Sax, M. / Yan, Y. / Jordan, F. / Guest, J.R. / Furey, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l8a.cif.gz | 340.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l8a.ent.gz | 270.3 KB | Display | PDB format |
PDBx/mmJSON format | 1l8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8a ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains a functional dimer, with the two identical molecules related by a non-crystallographic twofold axis. It also contains two thiamin diphosphate and two magnesium II ion cofactors. |
-Components
#1: Protein | Mass: 99657.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: JRG pGS878 / Production host: Escherichia coli (E. coli) / Strain (production host): JRG 3456 References: UniProt: P06958, UniProt: P0AFG8*PLUS, pyruvate dehydrogenase (acetyl-transferring) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.35 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.05 Details: PEG2000 monomethyl ether, propanol, sodium azide, Hepes buffer, magnesium chloride, thiamin diphosphate, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jan 27, 2000 / Details: toroidal mirror |
Radiation | Monochromator: curved silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 146183 / Num. obs: 146183 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.85→1.94 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.9 / Num. unique all: 13132 / Rsym value: 0.175 / % possible all: 70.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 528145 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 70.2 % / Rmerge(I) obs: 0.175 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.5 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 8
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Refinement | *PLUS Num. reflection obs: 125670 / Rfactor all: 0.198 / Rfactor obs: 0.192 / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.261 / % reflection Rfree: 6 % / Rfactor Rwork: 0.236 |